From 7054c5342f28f1b5ccb966919dc3a23f06206d0b Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Thu, 21 Jul 2011 12:13:29 -0400 Subject: [PATCH 3/4] When using the BWA bindings, you have to explicitly call close() to get the bindings to release memory. It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA. --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 3 +++ .../validation/ValidationAmpliconsIntegrationTest.java | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 14d462518..7e39d2658 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -228,6 +228,9 @@ public class ValidationAmplicons extends RodWalker { } public void onTraversalDone(Integer fin ) { + if(aligner != null) + aligner.close(); + validateSequence(); if ( doNotUseBWA ) { lowerRepeats(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java index 1829e9549..95f4ac0ae 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; */ public class ValidationAmpliconsIntegrationTest extends WalkerTest { - @Test(enabled=false) + @Test(enabled=true) public void testWikiExample() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; @@ -40,7 +40,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest { executeTest("Test probes", spec); } - @Test(enabled=false) + @Test(enabled=true) public void testWikiExampleMonoFilter() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; From 2f5d10d16bd9e53b293c1a913e9f7a3cd601784f Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 21 Jul 2011 13:21:48 -0400 Subject: [PATCH 4/4] Fix bug wherein aligner could be closed prior to its being used to lowercase sequences. --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 7e39d2658..cb03d4c61 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -228,14 +228,12 @@ public class ValidationAmplicons extends RodWalker { } public void onTraversalDone(Integer fin ) { - if(aligner != null) - aligner.close(); - validateSequence(); if ( doNotUseBWA ) { lowerRepeats(); } else { lowerNonUniqueSegments(); + aligner.close(); } print(); }